Two Chilean mummies hold the first genetic proof Europeans brought smallpox

Q: Why did smallpox kill such a large proportion of Indigenous people?

Indigenous populations had no prior exposure to smallpox, so their immune systems had no learned response. In immunologically naive populations, transmission is faster and mortality far higher than in populations with partial immunity from prior exposure.

Q: Will this approach find other colonial-period pathogens in the Americas?

The bioinformatic pipeline that found CAM9 screens for multiple pathogens simultaneously. The same dataset could reveal other diseases in the Camarones 9 population. Researchers have called for expanded analytical infrastructure across Latin America.

For five centuries, the worst epidemic in the history of the Americas had no molecular paper trail. Historical accounts described how the disease swept through the Aztec, Maya, and Inca empires; population records tracked the collapse; but the virus itself had never been recovered from the moment of first contact. Two mummies changed that.

Their bones, preserved in the extreme aridity of northern Chile, contained identifiable fragments of Variola major — the smallpox virus. The find is the first molecular evidence confirming that smallpox arrived in the Americas from Europe. The researchers, led by Bruno Romero González of Trinity College Dublin, recovered viral DNA so distinctive it required a new strain designation: CAM9.

How the viral DNA survived in bone

The two individuals — a woman estimated at thirty to thirty-five years old and a man around eighteen to twenty — were found at an archaeological site called Camarones 9, near the Pacific coast of northern Chile. Their preservation was natural: the region’s extreme aridity kept their remains intact long enough for organic material to survive at the molecular level.

The team was not originally searching for pathogens. Romero González was processing bone samples for population ancestry data when he applied a bioinformatic pipeline that scans raw DNA reads for pathogen signatures. The software found viral material in both mummies. When sequenced and compared against known variola genomes, the results placed both individuals as victims of the same outbreak — their viral genomes were nearly identical, ruling out separate exposures.

The work was conducted in close collaboration with Constanza de la Fuente Castro of Universidad de Chile, who noted the technical difficulty: working with ancient DNA that has accumulated chemical damage over centuries and exists in very low concentrations requires sensitive detection methods and careful phylogenetic analysis to avoid misclassification.

What CAM9 shows about the crossing

The new strain’s evolutionary position is the heart of the finding. In the viral family tree, CAM9 sits between the medieval European lineages documented before contact with the Americas and the later colonial-era variants found in other archival and mummified samples. That position is precisely where a newly arrived strain should appear: it had not yet accumulated the mutations that accumulated over generations of transmission in the Americas.

“Historical records can broadly capture what happened in the past, but they’re not necessarily super accurate on the local level,” said Dr. Shigeki Nakagome of Trinity College Dublin, a co-author on the study.

The evolutionary timeline that emerges from the data has three phases. Before European contact, smallpox evolved rapidly among dense Old World populations. During the peak colonial epidemics of the 17th and 18th centuries, the evolutionary rate slowed — the virus appears to have reached an optimum for transmission in populations with no prior immunity, and selection pressure temporarily eased. Later, as vaccination campaigns reduced susceptible hosts, the evolutionary pace increased again as the pathogen adapted to evade partial immunity.

The scale of the catastrophe these genomes represent

The epidemics smallpox enabled reshaped the demographic history of two continents. Estimates of total Indigenous mortality from the disease and the colonial disruption it facilitated run as high as ninety percent of the pre-contact population in the hardest-hit regions, with roughly four million deaths that can be attributed directly to the pathogen. The disease often preceded colonial armies, spreading through pre-existing Indigenous trading networks and reducing resistance before military confrontation.

The Camarones 9 site has no historical record of documented smallpox outbreaks, which raises a question the CAM9 genomes alone cannot answer: how did the virus reach so far south from its initial point of introduction? The researchers suggest it traveled along those same trade networks — consistent with the speed of epidemic spread visible in colonial records.

What this evidence still leaves open

The study’s foundation is two individuals from one site. That is enough to establish CAM9’s existence and evolutionary position, but not enough to determine how many separate introductions of smallpox occurred across the Americas, how rapidly it spread, or whether CAM9 represents the initial introduction or a subsequent wave.

Ancient DNA from samples this old is fragmented and exists in low concentrations, which means detection relies on computational tools trained on known pathogen families. A novel strain — as CAM9 was — requires careful phylogenetic placement before confident identification. Additional genomes from other sites and time periods will be needed to trace the full trajectory.

The date range of the two mummies — somewhere between roughly 1492 and 1631, a span of nearly 140 years — leaves temporal uncertainty about when precisely the Camarones 9 community encountered the outbreak. The site’s location near the Pacific coast suggests the virus may have arrived via maritime trade routes, but that pathway remains speculative without corroborating evidence.

Common questions about smallpox and the Americas

Why did smallpox kill such a large proportion of Indigenous people? Indigenous populations in the Americas had no prior exposure to smallpox or its close relatives, meaning their immune systems had no learned response. When a virus enters an immunologically naive population, transmission is faster and mortality higher than in populations that carry partial immunity from prior exposure. The scale of the mortality was the direct consequence of introducing a pathogen to a population that had never encountered it.

What is a viral phylogenetic tree and why does it matter here? Phylogenetics reconstructs evolutionary relationships by comparing DNA sequences across samples. Newer strains show fewer mutations from an ancestral sequence; derived strains carry more. CAM9’s position between pre-contact European strains and later colonial-era variants confirms it is an early arrival — not a re-introduction from a later wave. Its slot in the viral family tree was previously empty.

Will this approach find other colonial-period pathogens in the Americas? The bioinformatic pipeline that identified smallpox in the Camarones 9 samples was designed to detect multiple pathogens simultaneously. The same dataset that yielded CAM9 could contain evidence of other infectious diseases affecting the same population. The research team has called for increased funding and analytical infrastructure in institutions across Latin America, so that future findings from colonial-period archaeological sites can be analyzed and retained in the countries where the remains were found.

The study was published in Science. The CAM9 genome is expected to anchor further comparative work as colonial-period remains across the continent are screened using similar methods.

Reference: Romero González et al., “Ancient smallpox genomes reveal how European colonization brought the disease to the Americas,” Science, 2026. DOI: 10.1126/science.aee6957

Tags: archaeology, ancient DNA, Bruno Romero González, CAM9, Camarones 9, smallpox